Tertiary workflows for single-cell RNA-seq data


Tertiary workflows in single-cell RNA-seq analysis are, in the definition of the Human Cell Atlas (HCA), those processes occuring subsequent to quantification, such as clustering and trajectory inference. Example libraries implementing these analyses are Seurat, Scater and Scanpy.

This is a project to increase the re-usability and reproducibility of these workflows, to facilitate comparison and benchmarking. Our strategy is:

  1. Provide command-line access to individual library functions through simple wrapper scripts packaged with Bioconda.
  2. Enable pipeline inter-operability by adopting and/or improving file format standards (e.g. Loom) which can be read and written by a variety of packages.
  3. Facilitate the generation of workflows built on the above components, in environments such as Galaxy and Nextflow, for deployment in platform-agnostic ways.